Gene duplications allowed the acquisition of new functions, contributing to the diversification and morphological innovations of different animal lineages. For example, the acquisition and evolution of proteins that control the retinoic acid (RA) action during animal development has been related with the development of several vertebrate- and chordate-specific features, including the anterior-posterior axis formation or the neural differentiation and pattering.

It is know that RA is regulated at two levels: metabolism and signalling. We have focussed our analysis on several enzymes involved in retinoid metabolism. We have studied the medium-chain alcohol dehydrogenase (ADH) family and gathered data at the gene and protein level, exon-intron distribution, expression patterns, and genome and EST databases, in order to reconstruct the evolutionary history of ADH family in the animal kingdom. We have also analyzed the evolution of the retinol (RDH) and retinaldehyde dehydrogenase (ALDH1) families. We have reported novel RDH and ALDH1 members in deuterostomes. We have proposed a new phylogeny of the RDH enzymes and a model for the RDH expansion in vertebrates. Moreover, the analysis of the ALDH enzymes and other components of the RA pathway have allowed us to conclude that RA genetic machinery was already present during early deuterostome evolution, thereby calling into question its relationship with the origin of chordates. Currently, we pursue with these analyses extending them to other animal groups and to proteins connected to significant physiological and developmental processes in an attempt to investigate the relationship between gene family evolution and the acquisition of functional innovations of the organisms. Finally, we also analyse the structure, frequency, phylogenetic relationships and ability to transpose of one type of repetitive DNA sequences –the non-LTR retrotransposons– in amphioxus, ascidians and hagfish to find out how these elements have evolve and how they have contributed to the current structure of the chordate genomes.